I still think it's a good game, but it's not even in the top 5 best of the Zelda series, IMO. Even some of the 2D Zelda games have been more creative.
Just to clarify a few things, I enjoyed the visuals, as well as the expressive characters. I won't talk about the slow sailing, triforce quest or bosses being too easy because the HD version fixed that, but there are more fundamental flaws that an HD version simply cannot fix.
1. Predictable plot. Yes, WW is far from the only Zelda game to have the typical "rescue the princess. find artifacts in the dungeons. fight ganon". But Majora's Mask subverted this cliche to make a really unique and moving story. Then, WW reverted right back to it. Yes, I love the characters. It had great moments such as the Master Sword frozen in time and King Daphnes comparing himself to Ganon. Still, stale formula.
2. Sparse overworld. The feeling of sailing an ocean is fun, but once you remember where everything is, it feels like a Rube Goldberg device to get you where you want to go. In some sense, the minimalism is good, but overall, it feels like 90% of the visuals in this game are copied and pasted. If Twilight Princess bears the mark of big overworld with a bunch of empty space, so should Wind Waker.
3. Unoriginal items. The Deku Leaf is an obvious exception; I loved that one. But other than that, it looks like Wind Waker just took all of the staple Zelda items without adding great new ones or returning older favorites.
4. Predictable item usage. What I liked about many of the other Zelda games is that it's not always apparent where or how you need to use your items. In WW, you get an item and then use it where you are supposed to and nothing more. For example, in OOT, an arrow activated a twisted corridor. In Wind Waker, you use an arrow to activate a platform and that's it. Or a hammer smash an apparent obstacle and that's it.
5. Puzzles aren't that great. Puzzles are few are far in between in Wind Waker. If you count lighting readily visible torches to find a chest, moving blocks along a linear path or slaying enemies to find a key as a puzzle, you're in luck. If not, then there really isn't much innovation in the puzzle design.
6. Dungeons are simplistic. Dungeons in WW are typically small and not very complex. They are linear, and are often as easy as walking in a guided path. The look great visually, but they don't inspire the same humility as the giants of MM, TP and OOT.
7. Lack of enemy variety. Boss fights were great, but I'm talking about common enemies. Some of the dungeons have exceptions and the Darknuts are fun to fight, but the majority of the enemies in the game are just Chu's and Bokoblins. They're the equivalent Zubats and Ratattas in Pokemon.
All of my complaints seem to have a common theme (aside from me being whiny). The game is like a dumbed-down version of Ocarina of Time. Wind Waker's gameplay is as watered-down as it's Hyrule. Great visuals are great, but the gameplay just doesn't match up to the other Zelda games.